Ali Osman Berk Şapcı

Poster at ProbGen 2026

Tue, 10 Mar 2026 00:00:00 +0000

A poster on sequence distances and genome-wide phylogenetic pattern matching was presented at ProbGen 2026 (UC Berkeley). PDF.

SPrUCE published in Molecular Ecology Resources

Sun, 01 Mar 2026 00:00:00 +0000

SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation, with Daniel Melendez, Vineet Bafna, and Siavash Mirarab, appears in Molecular Ecology Resources.

krepp published in Genome Biology

Tue, 10 Feb 2026 00:00:00 +0000

krepp: A k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement, with Siavash Mirarab, appears in Genome Biology. Conference slides: RECOMB 2025.

Binning mitochondrial reads from skimming data using krepp

Wed, 17 Sep 2025 00:00:00 +0000

Binning mitochondrial reads from skimming data using krepp and all mitogenomes available on RefSeq.

Talks at IMSI workshop on alignments and phylogenies

Wed, 20 Aug 2025 00:00:00 +0000

At the IMSI program Contemporary Challenges in Large-Scale Sequence Alignments & Phylogenies (Chicago): a krepp tutorial (slides, recording); a short talk on discordant-region mapping (slides, recording); and a poster.

I presented our latest tool for phyloegentic placement in RECOMB 2025

Thu, 15 May 2025 00:00:00 +0000

I really enjoyed RECOMB 2025 in Seoul. This was my first time in East Asia. I somewhat enjoyed it. The conference coincided with Yeon Deung Hoe (perhaps on purpose?) and it’s been quite an experience. My slides are available here. …and a couple of photos: Yonsei University, Seoul, South Korea. I seem to make the same gesture (as seen above) during all my talks, constantly.

FlyVISTA published in Science Advances

Wed, 12 Mar 2025 00:00:00 +0000

FlyVISTA, an integrated machine learning platform for deep phenotyping of sleep in Drosophila, with Mehmet F. Keleş and colleagues, appears in Science Advances.

Our paper has been accepted in RECOMB 2025

Tue, 14 Jan 2025 00:00:00 +0000

Our paper titled “A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement” has been accepted in RECOMB 2025. I’m looking forward to my presentation in Seoul, which will be my first visiting East Asia.

We introduced a technique to estimate read-to-genome distances from k-mer hits. The idea is based on the search for matching k-mers up to a certain Hamming distance in a colored k-mer index, and then finding the maximum likelihood distance based on k-mer matches and corresponding distances for each hitting reference. These distances approximate alignment Hamming distance at the read level, and 1-ANI between a query genome and the matching reference(s) on average across all reads. We then propose an intuitive and accurate heuristic to place reads on an existing backbone phylogeny in a principled way using a likelihood ratio test.

Mapping mitochondrial baits to taxonomic groups using KRANK

Mon, 28 Oct 2024 00:00:00 +0000

Mapping mitochondrial baits to taxonomic groups using KRANK and all mitogenomes on RefSeq.

Our paper has been published in Genome Research

Thu, 29 Aug 2024 00:00:00 +0000

KRANK has been published in Genome Research (RECOMB 2024 Special Issue). The tool is available at GitHub, together with links to pre-built indexes of varying sizes, utilizing WoL reference database and a RefSeq snapshot. Using these indexes, KRANK showed superior performance in taxonomic classification and abundance profiling on CAMI benchmarking datasets to many existing methods. Here is the abstract: Using k-mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification.

basty for Behavioral Analysis of Sleep in Drosophila melanogaster

Sat, 06 Jul 2024 00:00:00 +0000

Quantifying animal behavior is the main objective of computational ethology. This task is not straightforward. From a computational perspective, it involves mapping spatiotemporal features, such as changes and postures, to behavioral categories.

I attended RECOMB 2024 and presented KRANK

Tue, 30 Apr 2024 00:00:00 +0000

I gave a talk on KRANK in RECOMB 2024. My slides are available here. In summary: This was my first time visiting Boston, and I enjoyed it very much. I think the organization was much better last year, in Istanbul. Poster sessions are definitely the best place to meet relevant people. Being the first speaker early in the morning was unfortunate, many people missed the entire (or a considerable portion) talk.

I gave a short talk in BioSys 2024

Sat, 27 Apr 2024 00:00:00 +0000

I presented KRANK in BioSys 2024 (Workshop on Emerging Computer Systems Challenges and Applications in Biomedicine) which held in conjunction with the ASPLOS 2024 (29th ACM International Conference on Architectural Support for Programming Languages and Operating Systems). Thanks to Yatish Turakhia and his students for the organization. My slides are available here, and the recording can be found here. A shot taken by Kyle Smith during the presentation, Hilton La Jolla Torrey Pines, San Diego.

CONSULT-II has been published in Bioinformatics

Sat, 16 Mar 2024 00:00:00 +0000

After a long review process, CONSULT-II finally appeared in Bioinformatics. I think CONSULT-II is conceptually very exciting but as a software I am not very proud of it. The implementation is very eclectic and not user-friendly at all. I was able to re-implement it for KRANK, and KRANK’s software offers the same functionality with an improved user experience and increased scalability. Another thing is that, CONSULT-II consists of many heuristics that there are alternatives for.

KRANK has been accepted in RECOMB 2024

Fri, 22 Dec 2023 00:00:00 +0000

Our paper titled “Memory-bound k-mer selection for large evolutionary diverse reference libraries” has been accepted to RECOMB 2024. Hopefully, I’ll be in Cambridge (April 29 - May 2, 2024).

MuDCoD has been published in Bioinformatics

Sat, 23 Sep 2023 00:00:00 +0000

We published a paper in Bioinformatics. We describe a new approach for community detection in multi-subject and dynamic networks, in particular networks constructed from scRNA-seq data. The abstract is given below, and see the figure for an illustration of what multi-subject and dynamic networks refer to. Motivation: With the wide availability of single-cell RNA-seq (scRNA-seq) technology, population-scale scRNA-seq datasets across multiple individuals and time points are emerging. While the initial investigations of these datasets tend to focus on standard analysis of clustering and differential expression, leveraging the power of scRNA-seq data at the personalized dynamic gene co-expression network level has the potential to unlock subject and/or time-specific network-level variation, which is critical for understanding phenotypic differences.

Our paper has been published in Natural Language Engineering

Tue, 06 Jun 2023 00:00:00 +0000

We just published a paper in Natural Language Engineering after a long revision process. This work was a continuation and an extension of my undergraduate graduation project.

CONSULT-II won the best paper award

Sat, 15 Apr 2023 00:00:00 +0000

I presented in RECOMB Comparative Genomics 2023, in Istanbul (see my slides). Our paper, with Elenora Rachtman and Siavash Mirarab, CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing won the best paper award.

CONSULT for Contamination Removal

Wed, 15 Feb 2023 00:00:00 +0000

Relying on locality-sensitive hashing, CONSULT-II k-mers from a query set and tests whether they fall within a user-specified hamming distance of k-mers in the reference dataset. Using this invaluable information, it can remove contamination, i.e., reads that do not belong to the reference set, at least predicted to do so.

I successfully defended my MSc thesis

Mon, 01 Aug 2022 00:00:00 +0000

I have finished my thesis, titled “Automated behavioral analysis of asleep fruit fly” – which is now available online, and obtained my MSc degree. The defense was on 26 July 2022, you can find my slides here. Jury members are listed below, I do appreciate their time and invaluable comments. Öznur Taştan, Sabancı Üniversitesi (advisor) Sündüz Keleş, University of Wisconsin-Madison (advisor) Onur Varol, Sabancı Üniversitesi Gözde Akar, Orta Doğu Teknik Üniversitesi Ercüment Çiçek, Bilkent Üniversitesi

I presented a poster and a spotlight presentation at MLCB 2021

Mon, 22 Nov 2021 00:00:00 +0000

I attended 16th Machine Learning for Computational Biology Conference (MLCB), and presented our work in progress, titled “MuDCoD: Multi-Subject Community Detection in Dynamic Gene Networks” (see my slides, note that I ended up using a simplified version due to limited time). The 2-page long abstract is not available online, but hopefully, a preprint will be soon. We also had a poster presentation on the second day.